Merge pull request #46 from HumanBrainProject/develop

fix releasing of inferred instances

Author: olinux

src/main/java/org/humanbrainproject/knowledgegraph/commons/propertyGraph/arango/control/ArangoNativeRepository.java

@@ -21,8 +21,6 @@
 import org.springframework.stereotype.Component;
 
 import java.util.*;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
 import java.util.stream.Collectors;
 
 @Component
@@ -43,11 +41,11 @@ public class ArangoNativeRepository {
     @Autowired
     ArangoRepository arangoRepository;
 
-    public Set<NexusInstanceReference> findOriginalIdsWithLinkTo(ArangoDocumentReference instanceReference, ArangoCollectionReference collectionReference) {
-        Set<ArangoCollectionReference> collections = databaseFactory.getDefaultDB().getCollections();
+    public Set<NexusInstanceReference> findOriginalIdsWithLinkTo(ArangoConnection connection, ArangoDocumentReference instanceReference, ArangoCollectionReference collectionReference) {
+        Set<ArangoCollectionReference> collections = connection.getCollections();
         if (collections.contains(instanceReference.getCollection()) && collections.contains(collectionReference)) {
             String query = queryFactory.queryOriginalIdForLink(instanceReference, collectionReference, authorizationContext.getReadableOrganizations());
-            List<String> ids = databaseFactory.getDefaultDB().getOrCreateDB().query(query, null, new AqlQueryOptions(), String.class).asListRemaining();
+            List<String> ids = connection.getOrCreateDB().query(query, null, new AqlQueryOptions(), String.class).asListRemaining();
             return ids.stream().filter(Objects::nonNull).map(NexusInstanceReference::createFromUrl).collect(Collectors.toSet());
         }
         return Collections.emptySet();

src/main/java/org/humanbrainproject/knowledgegraph/indexing/control/nexusToArango/NexusToArangoIndexingProvider.java

@@ -55,7 +55,7 @@ public Vertex getVertexStructureById(NexusInstanceReference incomingReference) {
     }
 
     public Set<NexusInstanceReference> findInstancesWithLinkTo(String originalParentProperty, NexusInstanceReference originalId) {
-        return nativeRepository.findOriginalIdsWithLinkTo(ArangoDocumentReference.fromNexusInstance(originalId), ArangoCollectionReference.fromFieldName(originalParentProperty));
+        return nativeRepository.findOriginalIdsWithLinkTo(databaseFactory.getDefaultDB(), ArangoDocumentReference.fromNexusInstance(originalId), ArangoCollectionReference.fromFieldName(originalParentProperty));
     }
 
     public Vertex mapToOriginalSpace(Vertex vertex, NexusInstanceReference originalId) {

src/main/java/org/humanbrainproject/knowledgegraph/releasing/control/ReleaseControl.java

@@ -203,8 +203,9 @@ public IndexingMessage release(NexusInstanceReference instanceReference, Integer
         payload.addReference(HBPVocabulary.RELEASE_INSTANCE, configuration.getAbsoluteUrl(instanceReference));
         payload.put(HBPVocabulary.RELEASE_REVISION, revision);
         payload.addType(HBPVocabulary.RELEASE_TYPE);
+        NexusInstanceReference originalId = nativeRepository.findOriginalId(instanceReference);
         NexusSchemaReference releaseSchema = new NexusSchemaReference("releasing", "prov", "release", "v0.0.2");
-        NexusInstanceReference instance = instanceManipulationController.createInstanceByIdentifier(releaseSchema, instanceReference.getFullId(false), payload, null);
+        NexusInstanceReference instance = instanceManipulationController.createInstanceByIdentifier(releaseSchema, originalId.getFullId(false), payload, null);
         return new IndexingMessage(instance, jsonTransformer.getMapAsJson(payload), null, null);
     }
 
@@ -215,8 +216,9 @@ public NexusInstanceReference unrelease(NexusInstanceReference instanceReference
             Object relativeUrl = document.get(ArangoVocabulary.NEXUS_RELATIVE_URL);
             if (relativeUrl != null) {
                 NexusInstanceReference fromUrl = NexusInstanceReference.createFromUrl((String) relativeUrl);
+                NexusInstanceReference originalFrom = nativeRepository.findOriginalId(fromUrl);
                 //Find release instance
-                Set<NexusInstanceReference> releases = nativeRepository.findOriginalIdsWithLinkTo(ArangoDocumentReference.fromNexusInstance(fromUrl), ArangoCollectionReference.fromFieldName(HBPVocabulary.RELEASE_INSTANCE));
+                Set<NexusInstanceReference> releases = nativeRepository.findOriginalIdsWithLinkTo(databaseFactory.getInferredDB(), ArangoDocumentReference.fromNexusInstance(originalFrom), ArangoCollectionReference.fromFieldName(HBPVocabulary.RELEASE_INSTANCE));
                 for (NexusInstanceReference nexusInstanceReference : releases) {
                     Integer currentRevision = nativeRepository.getCurrentRevision(ArangoDocumentReference.fromNexusInstance(nexusInstanceReference));
                     nexusInstanceReference.setRevision(currentRevision);